This is quite similar to the question I posted recently quoted below:
3) I also attempted to cluster the models with > dopehr_loopmodel.cluster(cluster_cut=1.5), which generated a representative > structure with the parts of the protein that remained similar in most of the > models but without the variable parts (files cluster.ini and cluster.opt). > Does it make sense to select the model that is closer to that consensus > structure? If yes is there a way to do it with Modeller? I know it can been > found with Maxcluster program. Or alternatively, do you reckon it is better > to select the model based on the normalized DOPE z-score? >
I'm also curious to read your comments.
2010/5/3 Jan H. Löhr loehr@chemie.uni-hamburg.de
> Dear Modeller users, > > according to posts in this mailing list as well as the background > information to ModLoop, the best loop-model is chosen by lowest > pseudo-energy score > (http://modbase.compbio.ucsf.edu/modloop/ - Fiser's and Sali's papers > cited > at the bottom of the page). > However, the tutorial of Modeller indicates that "it is important to note > that a most accurate approach to loop refinement requires the modeling of > hundreds of independent conformations and their clustering to select the > most representative structures of the loop" > http://www.salilab.org/modeller/tutorial/advanced.html). > > I have been comparing different loop-models generated by loop.model for a > selected region of a pdb-file and I am tempted to simply choose the best > DOPE-HR-scoring model. Yet the clustering idea does makes sense. So far, > the > greatest cluster of models often contains (one of) the best scoring > model(s), but not in every case. > > My question is therefore: Should the best model be chosen, or should the > best model of the greatest cluster be chosen? > > I wonder about your opinions regarding this issue. > In case anyone is voting for the clustering method: What method is easily > suitable for clustering - unfortunately, the loop.model-class does not seem > to have an integrated clustering option, does it? > > Regards > > Jan > > Jan H. Löhr > Univ. Hamburg, Germany > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >